Read RI values from comments field into RI field & added unit test

RIAssigner/data/Data.py

@@ -1,5 +1,6 @@
 from abc import ABC, abstractmethod
 from typing import Iterable, List, Optional
+import pandas as pd
 
 from pint import Quantity, UnitRegistry
 from pint.unit import build_unit_class
@@ -9,6 +10,7 @@ class Data(ABC):
     """ Base class for data managers. """
     RetentionTimeType = Optional[float]
     RetentionIndexType = Optional[float]
+    CommentFieldType = Optional[str]
     URegistry = UnitRegistry()
     Unit = build_unit_class(URegistry)
 
@@ -115,3 +117,36 @@ def retention_indices(self, value: Iterable[RetentionIndexType]):
             value (Iterable[RetentionIndexType]): Values to assign to property.
         """
         ...
+
+    @property
+    @abstractmethod
+    def comment(self) -> Iterable[CommentFieldType]:
+        """Getter for `comment` property.
+
+        Returns:
+            Iterable[CommentFieldType]: Comment field values stored in data.
+        """
+        ...
+
+    def extract_ri_from_comment(self, specific_string):
+        """ Extract RI from comment field.
+        Extracts the RI from the comment field of the data file. The RI is expected to be
+        in the format 'specific_string=RI_value'. The function extracts the RI value and
+        returns it as a list.
+
+        Parameters
+        ----------
+        content_comment:
+            Comment field of the data file. 
+        specific_string:
+            String that is expected to be in the comment field before the RI value.
+
+        Returns
+        -------
+            RI values as a list.
+        """
+
+        mask = pd.Series(self.comment).str.contains(rf'\b{specific_string}\b', na=False)
+        extracted_values = pd.Series(self.comment).str.extract(rf'\b{specific_string}=(\d+)\b')[0].astype(float)
+        self.retention_indices = extracted_values.where(mask, None).tolist()
+

RIAssigner/data/MatchMSData.py

@@ -70,9 +70,9 @@ def _read_retention_indices(self):
         """ Read retention indices from spectrum metadata. """
         self.retention_indices = [safe_read_key(spectrum, self._ri_key) for spectrum in self._spectra]
 
-    def _sort_spectra_by_rt(self):
+    def _sort_spectra_by_rt(self): 
         """ Sort objects (peaks) in spectra list by their retention times. """
-        self._spectra.sort(key=lambda spectrum: safe_read_key(spectrum, self._rt_key))
+        self._spectra.sort(key=lambda spectrum: safe_read_key(spectrum, self._rt_key) or 0) 
 
     def __eq__(self, o: object) -> bool:
         """Comparison operator `==`.
@@ -116,6 +116,38 @@ def retention_indices(self, values: Iterable[Data.RetentionIndexType]):
         else:
             raise ValueError('There is different numbers of computed indices and peaks.')
 
+    @property
+    def comment(self) -> Iterable[Data.CommentFieldType]:
+        """ Get comments."""
+        self.comment_keys = "comment"
+        content = [safe_read_comment_key(spectrum, self.comment_keys) for spectrum in self._spectra]
+        return content
+
+def safe_read_comment_key(spectrum: Spectrum, key: str) -> Optional[str]:
+    """ Read key from spectrum and convert to str or return 'None'.
+    Read the given key from the spectrum metadata and convert it to a string.
+    In case an exception is thrown or the key is not present, returns 'None'.
+
+    Parameters
+    ----------
+    spectrum:
+        Spectrum from which to read the key.
+    key:
+        Key to be read from the spectrum metadata.
+
+    Returns
+    -------
+        The key's value converted to string or 'None'.
+    """
+
+    meta_value = spectrum.get(key, default=None)
+    if meta_value is not None:
+        try:
+            meta_value = str(meta_value)
+        except ValueError:
+            meta_value = None
+    return meta_value
+
 
 def safe_read_key(spectrum: Spectrum, key: str) -> Optional[float]:
     """ Read key from spectrum and convert to float or return 'None'.
@@ -143,7 +175,6 @@ def safe_read_key(spectrum: Spectrum, key: str) -> Optional[float]:
             value = None
     return value
 
-
 def _assign_ri_value(spectrum: Spectrum, key: str, value: Data.RetentionIndexType):
     """Assign RI value to Spectrum object
 
@@ -153,4 +184,6 @@ def _assign_ri_value(spectrum: Spectrum, key: str, value: Data.RetentionIndexTyp
     """
     if value is not None:
         retention_index = ('%f' % float(value)).rstrip('0').rstrip('.')
+        if key == 'retentionindex':
+            key = 'retention_index'
         spectrum.set(key=key, value=retention_index)

RIAssigner/data/PandasData.py

@@ -45,7 +45,10 @@ def _init_carbon_number_index(self):
     def _init_rt_column_info(self):
         """ Find key of retention time column and store it. """
         self._rt_index = get_first_common_element(self._data.columns, self._rt_possible_keys)
-        self._rt_position = self._data.columns.tolist().index(self._rt_index)
+        if self._rt_index is not None:
+            self._rt_position = self._data.columns.tolist().index(self._rt_index)
+        else:
+            self._rt_position = None
 
     def _init_ri_column_info(self):
         """ Initialize retention index column name and set its position next to the retention time column. """
@@ -64,9 +67,11 @@ def _init_ri_indices(self):
             self._ri_position = self._rt_position + 1
             self._data.insert(loc=self._ri_position, column=self._ri_index, value=None)
 
+    # temporary adapted in case _rt_index is None
     def _sort_by_rt(self):
         """ Sort peaks by their retention times. """
-        self._data.sort_values(by=self._rt_index, axis=0, inplace=True)
+        if self._rt_index is not None:
+            self._data.sort_values(by=self._rt_index, axis=0, inplace=True)
 
     def __eq__(self, o: object) -> bool:
         """Comparison operator `==`.
@@ -116,3 +121,11 @@ def retention_indices(self, values: Iterable[int]):
             values (Iterable[int]): Values to assign.
         """
         self._data[self._ri_index] = values
+
+    @property
+    def comment(self) -> Iterable[Data.CommentFieldType]:
+        """ Get comments."""
+        self._comment_keys = "comment"
+        content = self._data[self._comment_keys].tolist()
+        return content
+

RIAssigner/data/SimpleData.py

@@ -1,5 +1,5 @@
 from copy import copy
-from typing import Iterable
+from typing import Iterable, Optional
 
 from RIAssigner.utils import is_sorted
 
@@ -51,3 +51,6 @@ def retention_times(self) -> Iterable[Data.RetentionTimeType]:
     def retention_indices(self, values: Iterable[Data.RetentionIndexType]):
         raise NotImplementedError()
 
+    @property
+    def comment(self) -> Iterable[Optional[str]]:
+        return None

tests/data/ri_from_comment/NIST_EI_MS_2mols.msp

@@ -0,0 +1,40 @@
+NAME: Water
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+NUM PEAKS: 5
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+16.0	8.99
+17.0	211.81
+18.0	999.0
+19.0	5.0
+20.0	3.0
+
+NAME: Methyl Alcohol
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+NUM PEAKS: 16
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+2.0	3.0
+12.0	2.0
+13.0	5.99
+14.0	15.99
+15.0	122.89
+16.0	1.0
+17.0	3.0
+18.0	6.99
+19.0	1.0
+28.0	44.96
+29.0	444.6
+30.0	63.94
+31.0	999.0
+32.0	742.33
+33.0	10.99
+34.0	1.0

tests/data/ri_from_comment/nist_to_ri_2mols.csv

@@ -0,0 +1,3 @@
+casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,
+7732185,5,Water,,H2O,9,"SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67",InChI=1S/H2O/h1H2,O,18
+67561,16,Methyl Alcohol,,CH4O,32,"SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806","InChI=1S/CH4O/c1-2/h2H,1H3",CO,32

tests/data/ri_from_comment/peaks_with_rt_ref_SemiStdNP.csv

@@ -0,0 +1,3 @@
+casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,Unnamed: 10
+7732185,5,Water,317.0,H2O,9,"SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67",InChI=1S/H2O/h1H2,O,18,
+67561,16,Methyl Alcohol,354.0,CH4O,32,"SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806","InChI=1S/CH4O/c1-2/h2H,1H3",CO,32,

tests/data/ri_from_comment/peaks_with_rt_ref_SemiStdNP_msp.csv

@@ -0,0 +1,43 @@
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+COMPOUND_NAME: Water
+RETENTION_INDEX: 317
+NUM PEAKS: 5
+16.0        8.99
+17.0        211.81
+18.0        999.0
+19.0        5.0
+20.0        3.0
+
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+COMPOUND_NAME: Methyl Alcohol
+RETENTION_INDEX: 354
+NUM PEAKS: 16
+2.0         3.0
+12.0        2.0
+13.0        5.99
+14.0        15.99
+15.0        122.89
+16.0        1.0
+17.0        3.0
+18.0        6.99
+19.0        1.0
+28.0        44.96
+29.0        444.6
+30.0        63.94
+31.0        999.0
+32.0        742.33
+33.0        10.99
+34.0        1.0
+

tests/data/ri_from_comment/peaks_with_rt_ref_StdNP.csv

@@ -0,0 +1,3 @@
+casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,Unnamed: 10
+7732185,5,Water,323.0,H2O,9,"SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67",InChI=1S/H2O/h1H2,O,18,
+67561,16,Methyl Alcohol,379.0,CH4O,32,"SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806","InChI=1S/CH4O/c1-2/h2H,1H3",CO,32,

tests/data/ri_from_comment/peaks_with_rt_ref_StdNP_msp.csv

@@ -0,0 +1,43 @@
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+COMPOUND_NAME: Water
+RETENTION_INDEX: 323
+NUM PEAKS: 5
+16.0        8.99
+17.0        211.81
+18.0        999.0
+19.0        5.0
+20.0        3.0
+
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+COMPOUND_NAME: Methyl Alcohol
+RETENTION_INDEX: 379
+NUM PEAKS: 16
+2.0         3.0
+12.0        2.0
+13.0        5.99
+14.0        15.99
+15.0        122.89
+16.0        1.0
+17.0        3.0
+18.0        6.99
+19.0        1.0
+28.0        44.96
+29.0        444.6
+30.0        63.94
+31.0        999.0
+32.0        742.33
+33.0        10.99
+34.0        1.0
+

tests/data/ri_from_comment/peaks_with_rt_ref_StdPolar.csv

@@ -0,0 +1,3 @@
+casno,num_peaks,compound_name,retention_index,formula,id,comment,inchi,smiles,nominal_mass,Unnamed: 10
+7732185,5,Water,1053.0,H2O,9,"SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67",InChI=1S/H2O/h1H2,O,18,
+67561,16,Methyl Alcohol,903.0,CH4O,32,"SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806","InChI=1S/CH4O/c1-2/h2H,1H3",CO,32,

tests/data/ri_from_comment/peaks_with_rt_ref_StdPolar_msp.csv

@@ -0,0 +1,43 @@
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+COMPOUND_NAME: Water
+RETENTION_INDEX: 1053
+NUM PEAKS: 5
+16.0        8.99
+17.0        211.81
+18.0        999.0
+19.0        5.0
+20.0        3.0
+
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+COMPOUND_NAME: Methyl Alcohol
+RETENTION_INDEX: 903
+NUM PEAKS: 16
+2.0         3.0
+12.0        2.0
+13.0        5.99
+14.0        15.99
+15.0        122.89
+16.0        1.0
+17.0        3.0
+18.0        6.99
+19.0        1.0
+28.0        44.96
+29.0        444.6
+30.0        63.94
+31.0        999.0
+32.0        742.33
+33.0        10.99
+34.0        1.0
+

tests/fixtures/mocks/DataStub.py

@@ -7,7 +7,8 @@ class DataStub(Data):
     def __init__(self, retention_times: Iterable[float], retention_indices: Iterable[float]):
         self._retention_times = retention_times
         self._retention_indices = retention_indices
-
+        self._comment = []
+
     def _read(self):
         pass
 
@@ -29,3 +30,7 @@ def retention_indices(self) -> Iterable[Optional[float]]:
     @retention_indices.setter
     def retention_indices(self, value: Iterable[float]):
         self._retention_indices = value
+
+    @property
+    def comment(self) -> Iterable[Optional[str]]:
+        return self._comment